Misunderstanding
by a. loquita
Summary: Sheppard sighed in dreaded agreement. Why was I afraid of this the moment Zelenka mentioned that part about a venomous snake creature on this planet...
1. Chapter 1

**Misunderstanding **(AKA: The Toilet Episode)

By: a. loquita

Summary: Sheppard sighed in dreaded agreement. "Why was I afraid of this the moment Zelenka mentioned that part about a venomous snake creature on this plant..."

Rating: K+

Spoilers: Sateda, Adrift, Lifeline, Tabula Rasa, The Seer

**TEASER**

In the women's restroom just off the Gate room, Teyla looked at Colonel Carter through their reflections in the mirror as she spoke. "And you did not say anything to him in response?"

Carter admitted, "That's when we were interrupted."

"When do you expect to speak with him again?"

"Soon. As soon as I work up the courage."

Teyla retuned a sympathetic look as Carter twisted the knob to turn on the sink. Just as the water started, it turned green.

"Ah," said Carter, "that can't be good."

Teyla heard a sound near the rows of stalls and moved to investigate. In one of them, there was not only green water coming up but there were also lizard or snake-like creatures filling the toilet as well. They flooded onto the floor and Teyla jumped back.

She said, "Colonel, I believe you need to see this."

**ACT 1**

McKay was in the infirmary, lying on his stomach. A curtain pulled across prevented Sheppard from seeing McKay's naked bottom half where Keller was working with some gauze and alcohol.

McKay complained loudly, "Why does this always happen to me?"

"You were gathering Intel," Sheppard said.

"And how do you figure that?"

"You, being the one who happened to be on the toilet when they came up. And now we know they bite."

McKay grouched, "Fabulous." Keller fought off a smile while listening to the banter between the two teammates.

"Look at this way," Sheppard said. "At least this time it was the other… side."

McKay rolled his eyes. "Yes, yes, let's all recall with fondness the time I was shot in the ass with an arrow."

Keller tilted her head, looking down at McKay's back end. "You'll have matching scars, one on each cheek." She grinned.

"You all laugh," McKay pointed out, "until I start turning into a snake. Then we'll see how funny this is."

Dr. Keller said reassuringly, "I'll run your blood and tissue sample immediately. If you start experiencing any strange symptoms let me know. But according to your scans, everything seems normal."

From the radio in Sheppard's ear Carter interrupted and asked, "How's Rodney doing?"

Sheppard pushed the button to respond. "He'll live."

"Good," said Carter. "Teams are gathered and ready to start scouting the city to try and find out what's going on. I want you in a Jumper along with your team."

"Minus the walking wounded, Dr. McSnake, I presume."

Carter heard the teasing nature in his tone and answered with a smile, "Yes."

"Copy that, on my way."

A short time later, Sheppard, Teyla, and Ronon were in one of the Jumpers flying underwater. They were surveying parts of the exterior of the city that lie below the surface. Everything appeared normal until they come upon an inlet pipe. Snakes seemed to be everywhere in the water, slithering up to and inside the pipe.

Sheppard said, "Well, now we know how they're getting in."

"But where are they coming from?" Ronon asked.

Sheppard turned on the brighter spotlight so they could see more clearly in the deep water. The line up of swimming creatures could be seen as far off in the distance as the light allowed.

Teyla commented first. "It appears they are coming from the direction of the mainland."

Sheppard sighed in dreaded agreement. "Why was I afraid of this the moment Zelenka mentioned that part about a venomous snake creature on this plant..."

A short time later, Cater and key leaders of the expedition were gathered in the conference room to assess the situation.

McKay reported, "We've got the pipes sealed off and shut down the filtration system. But a lot of them got in before we could do it."

"How many?" Sheppard interrupted.

"Oh, I don't know," McKay responded with usual acidity. "How does one measure an accurate amount of evil alien creatures? By the metric ton, or do you prefer in ounces?"

"McKay," Sheppard complained.

"A lot got in. Enough that we've had to seal off all the bathrooms and the kitchen in the commissary and so far they're not everywhere but… a lot."

Dr. Keller broke in at this point. "My main concern is that we have limited time before dehydration will begin to set in if we do not have a clean water source."

"We have reserves," Carter said.

"Yes, but they first need to be tested and even if they are still good, they won't last long."

"How much time?" Carter asked.

"A few days," Keller shrugged. "Depending on what else crops up."

"Crops up?!?" McKay questioned with growing concern.

Dr. Keller gave him a sympathetic smile. "Something else always crops up."

Carter redirected the conversation. "John, any insight on what's going on, where they've come from, and why?"

"Teyla, Ronon, and I believe they're coming from the mainland. We should take a closer look."

"OK," Carter said, "you three and Dr. Zelenka take a Jumper to the mainland. Surveillance only and check in every two hours. McKay, search the ancient database, see if there's any reference to an event like this." The meeting ended and everyone headed off to their duties.

TBC…


	2. Chapter 2

**ACT 2**

McKay was lying on his side on the floor of Katie Brown's lab. It was the only comfortable position he could find given his injury, and unfortunately, he knew this from plenty of past experience.

Katie had offered to help Rodney, watch over him, and get whatever he needed. But she also had work to get done so they compromised on him visiting her lab. Katie could keep an eye on the patient and her experiment.

McKay was multitasking. He was doing key word searches on parts of the database downloaded on to his laptop. The idea was that perhaps these creatures, or some closely related relatives, were indigenous to many worlds and had been studied at some point. Any mention of them at all might give them a clue as to what was currently happening on Atlantis. While running the searches, McKay was also entertaining both himself and Katie with commentary on more exciting topics.

"King Tut was great, but by far my favorite was Egghead." McKay concluded and looked at Katie expectantly.

"I have to admit, Rodney, I never watched the show."

"Never watched it?" McKay seemed stunned by the suggestion. "But it was one of the best things on television, ever."

"Mother never allowed us to watch much TV growing up."

"Oh." McKay was about to say more when he was suddenly distracted.

"What is it?" Katie asked, recognizing the change in his expression.

From his vantage point on the floor, McKay had a unique perspective. "I think one of those snakes is doing something to one of your plants."

"What? No, they'll ruin my polarization experiment."

By examining the situation it didn't take long for Rodney to determine that one of the creatures might have traveled through the ventilation system from the military living quarters' bathrooms on the floor below. But however it managed to travel, it was now on the bottom rung of a shelving unit containing rows and rows of plants.

"We'll have to shut down the ventilation then." Katie said distraught by the thought of more ruined experiments.

"Not yet," McKay said absently, "no real evidence that is how it got here." He was completely fascinated by the sight before him.

The creature broke into tiny parts, much like a lizard losing limbs before regenerating them. It then dug those tiny bits into the soil to the root system of one of the plants. McKay walked over, leaned down, and ripped off a leaf.

"Hey!" Katie protested.

He glanced at her and then back at the leaf in his hand. "I want to get a look." He motioned to the microscope on her lab bench.

She took the leaf and examined it under the scope, tiny black moving organisms seemed to be endocytosed by chloroplasts. "Amazing," Katie declared.

"Yeah?"

Katie moved aside so McKay could look. Meanwhile she explained, "There's a marine creature on Earth that has chloroplasts in its fins. They help to supply food to the animal much like they normally supply energy to plants. It's incredible, this is almost as if… it's in reverse."

McKay concluded for her, "But not unique to Earth, apparently, there's something similarly related in the Pegasus Galaxy."

She met his eyes, "Apparently."

Sheppard flew the cloaked Jumper low over the landscape. As they descended, the sight was surprising, dried and dying trees and plants were everywhere.

Ronon commented first, "Wasn't like this before."

"No, it wasn't," agreed Sheppard. "Wonder what happened?"

Zelenka suggested, "Drought?"

Teyla nodded at the possibly. "We've been here many months and in that time, have experienced only two or three rainy days."

Sheppard navigated the Jumper around dry, brittle trees. "If you're about to suggest that a big storm would solve all our problems. I just want to preemptively vote against that plan. Just something about… been there done that."

Teyla gave him a small smile in acknowledgment. Then returned the conversation to their current ordeal. "It could also be some sort of disease killing the plant life on this plant."

Zelenka considered it for a moment. "But then why aren't the plants on Atlantis dying? If it were a disease, surely it would have spread there by now?"

"Either way," Ronon interrupted. "Doesn't explain why those things came through the water and are on Atlantis now."

Sheppard flew the Jumper out of the trees and into a field. In the middle, up ahead was a large shape. It was moving up and down in the center almost as if it were breathing.

As they got closer, all four in the Jumper were bewildered into silence. Eyes wide, they observed a creature the size of a small house. It was almost whale-like in appearance, black skinned, and a large mouth at one end that opened and closed a few times. Near the middle, the gut was split open and small snakes identical to the ones now spreading throughout Atlantis were spilling out. They slithered across the parched, brown grass and into the ocean.

"That's where they're coming from," Sheppard stated the obvious.

"Is it… wounded?" Zelenka asked.

"Or giving birth," Telya offered.

As Sheppard flew the Jumper closer, the creature seemed to become agitated. It lifted its head and swung it around, moving and thrashing it's body. Though cloaked, Sheppard assumed somehow the creature sensed their presence and didn't like it. He radioed Atlantis.

"Atlantis base, this is Jumper One."

"Go ahead." The familiar voice of Colonel Carter immediately responded.

"I think we've found our point of origin. We're headed back to Atlantis."

"OK, see you soon. Carter out."

Meanwhile, in the lab of Katie Brown, McKay observed one of the small versions of the creatures now captured in a glass aquarium.

"Why isn't it going for it?" McKay wondered aloud. They'd placed a piece of lettuce inside the aquarium but the creature had shown absolutely no interest in it.

Cater entered the lab, "How's it going?"

"Slow progress," McKay said.

"Sheppard just check in, they are on the way back and he says they've got something."

"Did he say what?"

"He'll brief us when they get here." Carter turned to Dr. Brown and asked, "What about you two, have you found anything more?"

Katie replied, "This one doesn't seem interested in any of the things we've offered it. Pieces of bark, bits of root, leaves of lettuce. Nothing."

"It doesn't make sense." McKay shook his head. "We saw the other one of them fall to tiny pieces and… merge… with that plant and yet-" He threw up his hands at the glass aquarium. "Maybe this one is defective."

"Wait," something started to occur to Carter, "the other one merged with a plant that was in a pot, well watered, and under a light source, correct?"

McKay looked at Carter, at Katie, back again, and then began snapping his fingers. "That must be it," he said excitedly and went over to Katie's lab bench to get another potted plant.

Katie realized what his intentions were. "Wait, Rodney, my experiment!" She grabbed the plant from his hand and swapped it with one that was sitting on her desk.

"Little Rodneyanivalosa?!?" whimpered McKay.

Katie placed the cactus inside the aquarium. Immediately the creature broke apart, as they'd seen before, and it burrowed tiny pieces of itself into the dirt. McKay watched the process he'd already observed once before, this time with decidedly less excitement. "I feel so used."

Katie put her hand on his arm and patted it. "It's OK."

Carter grimaced as she watched. "So, not a defective one, I take it?" She could even make out movements along the surface if she looked closely, as if tiny worms where traveling just underneath the skin of the plant.

"Yeah," McKay said, "that's exactly what happened to the last one. The creature must sense when the plant is alive and growing, versus just a leaf or piece of the root."

"Well, the good news is," Carter pointed out, "our food stores are safe. Every fruit and vegetable on Atlantis will be a turn off for these creatures."

Katie sadly noted, "My poor plants are what they are after."


	3. Chapter 3

**ACT 3**

The entire team gathered in the conference room. Sheppard briefed them about the big mother snake spawning, the apparent massive drought that made all the vegetation go dry, and oh by the way, it looked like the mother snake was dying.

"Dying?" Keller asked. "How do you know?"

"What with my extensive expertise in giant snake medicine…" Sheppard said. Then relented, "Let's just say I have a hunch. It didn't look like she was in good shape."

Teyla offered up her opinion. "I do not see an obvious connection between the drought and these creatures coming to Atlantis. But it is difficult to believe it is mere coincidence."

"I agree," said Carter. "Dr. Brown and McKay's findings might provide a possible connection."

McKay spoke up, "They seem to merge with live plants but not pieces of a plant, or anything dead. So, for example, the dying vegetation on the mainland might–"

Sheppard interrupted, "What do you mean merge?"

McKay clicked a button on a remote and the monitors in the room came to life. A video of the creature in the glass enclosure appeared. Everyone in the briefing watched the process that McKay and Katie had seen twice now. Ending with a microscope image of tiny black specks wiggling around inside the cells of the plant.

McKay picked back up with his narrative. "You see, it's very interesting, according to Endosymbiotic Theory–"

Ronon interrupted, "What does this mean for us?"

"Well," McKay thought for a moment, "for one, the commissary can continue to serve buttered corn on Salisbury steak night."

Carter took a deep breath and redirected the conversation. "Presumably, once the plants began dying on the mainland, this 'mother' creature could sense a food source here on Atlantis. It couldn't come here itself so, perhaps as Teyla suggested, it began spawning."

"They came here looking for food?" Teyla reiterated, "And they are feeding on the plants from the inside out?"

McKay clarified, "We're not sure, but we're operating under that theory."

Carter asked the room for ideas. "Is there a way we can lure these things back to the mainland? Something that would attract them in that direction and not this one."

Sheppard offered, reluctantly, "Giant watering can?"

McKay said, "Other than waiting for grass to grow, literally, I don't know what else they want or need."

"Now that we're pretty sure they're not after hurting us," Lorne jumped into the conversation at this point, "my team can start attempting to flush the water inlet and filtration systems out and contain the creatures in holding crates. But it's going to be a slow process."

"Understood," Carter said and turned to her chief medical officer. "Anything else from your end, Dr. Keller?"

"The good news is testing on the city's back-up water supplies show it's untainted. We've begun rationing fresh water and the salt water from the ocean can be brought in and used for bathing. I think we should last 4 maybe 5 days before we run out of drinking water, unless we have the filtration up and running by then."

Teyla offered, "We may consider turning to some of our trading partners for fresh water."

Carter nodded. "Let's hope it doesn't become necessary. Lorne and his team may be able to complete their work before then. Meanwhile, let's continue to use caution. It doesn't appear they are harmful to anything other than the botany department, but I don't want us taking anything for granted."

"One did try to eat me," McKay reminded everyone.

"Maybe not," Sheppard suggested. "Maybe it just needed to get your butt out of the way before it could slither off to find a plant."

Following the briefing, Carter accompanied Doctors McKay, Brown, and Zelenka down to the lab. Even after months on the job, it was still difficult for her to fight instinct built from more than a decade of being in the thick of scientists when problems needed solutions. By the time they entered the lab, Carter's brain rebooted and she mentally kicked herself. She should be headed to her office right now, not here.

Katie mentioned to Zelenka, "Those results should be in," and the two went into an adjoining lab.

Carter started to leave but McKay said, "This must be hard on you." He had sympathy in his tone.

She asked, "Why?" Turning to face him, she wondered if McKay could identify with her struggle. He loved science as well, and felt safest in the lab working on something. Maybe he genuinely was concerned for her as a friend, was sympathetic to her effort to shed her old comfort zone and adjust to her newer, unfamiliar role.

He answered as if it were obvious, "To be forced to watch me and my girlfriend together..."

"Rodney," Carter blinked a few times, not even sure where to begin. "What makes you believe that I'm even single?"

It seemed like a reasonable thing to use to cut off McKay. But as soon as his expression changed, Sam regretted admitting it. He asked, "You're not?"

"Look, let's stay focused on the–"

"Who?" McKay asked.

Carter put on her 'I'm forcing myself to be patient with you' smile.

"Who?" McKay asked again.

There was a long, awkward pause between them. It wasn't a secret but in that moment, for Carter, it felt like she was revealing highly classified information. Perhaps that was why she leaned in to whisper the name.

Katie rounded a corner and re-entered her lab. She stopped short when she saw Colonel Carter back away from Rodney. They weren't embracing or anything, but from Katie's perspective it appeared that Carter had perhaps just kissed Rodney on the cheek. She wasn't positive though.

McKay had a look of frozen shock on his face. He stuttered when speaking to Carter. "But, but… him? He's not smart enough for you."

Zelenka entered behind Katie and held up a piece of paper. "Here it is," he said, a computer printout with code on it was in his hand.

Carter turned to him. "Those are the results of the test? Already?"

"Katie and I finished as quickly as we could and we ran the reactions twice so we're very certain."

"Yes, yes," McKay said anxiously. He was suddenly fully recovered from his surprise and focused on the problem at hand again. If only Zelenka to get on with it. "What does it say?"

Zelenka announced, "Testing shows these creatures on Atlantis are genetically related to the Goa'uld."


	4. Chapter 4

**ACT 4**

McKay looked panicked. "We've got Goa'uld symbiotes crawling around loose?"

Carter spoke up, "Not necessarily, McKay. They had opportunities but haven't done much of anything to any of us."

Zelenka nodded. "They might have come to Pegasus early and evolved on an entirely different evolutionary path."

"Could your team run the test again," requested Carter, "but this time against a sample of DNA from the Unas?"

McKay agreed with Carter's the idea, "Makes sense. Perhaps they are more closely related to the primitive form."

"If it merges with something that's ripped off a plant," Katie spoke up, obviously thinking out loud, "like a leaf or something, then the creature dies in a few days when that piece of lettuce does. It stands a much better chance of long-term survival if it's part of something that's living. Perhaps it is a true symbiotic relationship?"

Carter picked up on the reasoning. "See if it's doing any harm to the plants after merging with them, or if it's helping." When Carter subsequently returned to her office, John Sheppard entered just after her.

"I…ah," he gathered his thoughts. "Can I ask you something?"

"Of course."

"I know it seems that this thing is going after the botany department, and not our vegetables. But I can't help but wonder… this wouldn't be an attempt by one of our enemies to try to taint our food supply?"

"I thought of that too," she admitted, while sitting down.

"And the fact that the human form replicators used the same tactic against the wraith..."

"Are you suggesting they could be behind this?"

"Or the wraith, who got the idea once it started happening to them."

Carter looked doubtful. "Seems like a long, drawn out plan, and not exactly the wraith's style."

Sheppard gave in, "Yeah, I know. I just…"

Carter nodded. "Hard to believe it could be as simple as we picked the wrong planet to land on?"

"Something like that."

As Katie and McKay worked in the lab side-by-side, she suddenly turned to him. "It's funny, when I came in earlier it looked as if Colonel Carter had kissed you."

"What?"

"On the cheek."

McKay blinked at her. "No, she whispered something… actually, it's interesting..." Rodney seemed to catch himself. "Ah, but probably not something I should spread around."

"Oh, good. I mean, good that she wasn't… you know." Katie smiled and went back to working quietly. Rodney glanced at Katie a few times, then followed suit.

But only a few minutes later, Katie turned to him again. "Is Colonel Carter…Is she an ex-girlfriend?"

"What? No." McKay squinted, thought for a second and conceded, "Well, not exactly."

"Not exactly? What does that mean?"

McKay stumbled over the explanation at first, before his self-confident ego re-engaged. "We, ah, never actually dated. She wanted to but I, well, I told her it would never work. Still, I always suspected she held a torch for me."

Katie's eyes widened. "You think she still likes you?"

McKay backtracked, "I don't think so."

Katie looked a little relieved. But McKay could still sense concern on her part. "I promise you, Katie, Dr. Rodney McKay is a one woman man. Got that?"

She smiled, "Got it."


	5. Chapter 5

**ACT 5**

Lorne and his team hauled another crate up from the water with ropes that hung from a Jumper. He turned to Sheppard in the cockpit. "Kinda like big lobster traps."

Sheppard grimaced, "I think I'll pass on eating these guys."

Lorne gave a hint of a smile. Ronon asked, "What are lobsters?"

"Food fit for kings, my friend," Sheppard replied as he swung the Jumper around and headed to the mainland with yet another round of dead symbiotes to dump there.

Later, all the department heads were once again in conference to review where they now stood.

"The Ancient database does talk about an event that sounds similar, a breeding event that happens approximately every 100 years or so on a nearby planet, with harmless creatures that live off plants," reported McKay.

Zelenka added, "We previously assumed 'living off' meant eating, as in vegetarians. But now we think it is in reference to a symbiotic relationship."

"It just so happens that this century the event coincided with a drought. Probably forcing the symbiotes to seek whatever live plants they could find. Which happened to be here on Atlantis."

Zelenka picked up his turn. "We don't expect any further activity from them for another 100 years. They should live harmlessly in the plants until the time that they sort of swell up, grow, all in preparation for the next breeding event."

"Right," McKay said. "But we've got some time. Relatively."

Lorne reported his progress as well. "The system is nearly finished being flushed, most all of the symbiotes have died in that time."

"Perhaps," McKay hypothesized, "they could only survive so long without taking a host."

"Similar to the Goa'uld in that respect," added Carter.

Dr. Keller jumped in at this point. "As you all know an event a few weeks ago led us to learn that Colonel Carter can't be feed upon by wraith because of the naquada in her bloodstream. Katie, Rodney, and I believe that with further research on this creature genetically related, we may come up with something that could provide us with immunity to being feed on by the wraith. It'll take some time but it is promising."

"You know what they say," Sheppard quipped, "the best offence is a good defense."

Carter smiled. She felt that was a nice positive note to end the meeting on. "Great work everyone. Thank you."

After exiting the meeting, all went in different directions. But Teyla followed Carter into her office.

"I find it very ironic," Teyla said, "that it did not end up being a creature that would hurt us after all. In fact, not only can we peacefully coexist, depending on Dr. Brown, Dr. McKay, and Dr. Keller's research developments, these symbiotes might actually help us one day."

"Not everything is out to get us," Carter summarized.

"And that is a relief." Teyla suddenly spotted a new potted plant on the Colonel's desk. "A reminder perhaps of that lesson?"

"Perhaps," Carter said. "It was also a gift."

Teyla smiled knowingly, putting two and two together. "I assume this means your problem with a particular individual has also been resolved as well?"

"Everything's fine. It was a simple misunderstanding."

Teyla nodded. "I am happy to hear that."

"Me too."

fin

Thanks for reading!


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